Encoded
by PottsXStark
Summary: A criminal creates a special chip that is able to hold inside a real live person to succeed in creating a real life A.I. Pepper accidentally turns into a digital coded A.I human and now Tony has to figure out how to get her out until he encounters a problem that sticks him deeper into the mud puddle.
1. Chapter 1

**(One of the stories I promised. I have got to start updating I know XP) **

The trio spent their Saturday cooped up in the armory, something they did most often. Rhodey was studying non stop for his math final while Pepper was sitting upside down on her chair and Tony was doing armor upgrades.

"I'm. So. Bored" Pepper said.

"You do know if you stay like that your going to pass out?" Tony said.

"But it's fun!" She said.

"If you pass out your going to fall and crack open your head" He said.

"Whatever..." She crossed her arms.

About three minutes passed he then put down his tools and walked over to her. He crouched down to her head level.

"Feeling light headed yet?" He asked.

She shook her head.

"You know your forehead is red right?" He asked.

She rolled off the chair resulting her to fall on the floor.

"My head hurts..." She said.

"Don't doubt me next time" he said then patted her back.

Her phone started ringing and flashing an alert.

She sat up and reached for it. It was sitting on the arm of the chair. She looked at the lock screen and read her reminder and immediately smiled when she read the first word.

"What's up?" Tony asked.

"I have a job to do" She said.

"Which is?" He asked.

"It's for the FBI nothing special" she said smiling as she got up and grabbed her school bag.

"Your doing a case for the FBI?!" He asked.

"Well it's a case my dad is on, they suspect this guy who's been kidnapping teenage girls and locking them up in his basement also making illegal software and I'm supposed to be undercover" she said.

"That sounds more like bait to me" Tony said.

Rhodey looked up from his book and started cracking up along with Tony.

"He gets it" he said.

"Oh shut up I'm just happy I can finally do some FBI work" she said.

"Well Pep I'm not sure you should be doing this I mean I'm kinda shocked that your dad actually allowed you to do this?" He said.

"Lets just say it took a lot of kissing up and convincing, and hey I'm 19 I think I should be allowed to do this stuff, the FBI states you must be 18 and up to do this stuff" she said.

"Besides I'm not going unarmed" she said.

"What are you taking?" He asked.

"The arm of my suit" she said.

"So if he touches you, you're going to blow his head off?" He asked.

"Indeed" she said.

"Oh and I hope you don't mind I took one of your special inventions...the invisible chip" she said.

"For what?" He asked.

"I'm wearing a dress I need to conceal the arm somehow" she said.

"How about I just watch you from the sky" he said.

"Quit worrying ill be fine, if he touches me the wrong way ill just slap him with the arm piece which will hurt really bad" she said.

"I'm still keeping an eye on you" he said.

"Do as you please" she said then stuffed the arm piece of her suit into her bag and left.

He stuck his tongue out to the direction she walked.

"I think I will" he said.

...

Pepper walked down through the crowded New York side walk to one of the FBI secret hideouts. She turned left into an alley then found a stair case going down. She walked down then lifted up a tab and scanned her index finger on the pad. The door clicked signifying it was unlocked. She opened the door and closed it behind her. She saw people at their desks typing and talking on head sets. The place was very dark all they had for light was a few dimmed lamps and their computer screens.

"Patricia" said Virgil walking up to her.

"It's Pepper dad..." She said.

"Nows not the time for nicknames this is business" he said.

"It's my middle name..." She said.

"Look we got to be out of here by nine and it's eight fifty! You begged for this job now live up to it! Go get dressed" he said.

"Well someone's grumpy..." She said as she walked to the bathroom.

She locked the door behind her then opened up her backpack.

"Lets see...shirt...vest..." She said checking her items.

She first put on a black tank top then over that her bullet proof vest. She wore regular jeans and converse with a long black coat. She installed the chip into her suits arm and slipped it on. It instantly became invisible. She clenched and in clenched her fist.

"Perfect" she said then exited the bathroom.

"Alright people its time to move I need group V" said the director of the facility.

"Come on" Virgil said.

Four people met up outside the building not including Virgil and Pepper.

"Alright Miss Potts is going to draw in the suspect" said the head of the group.

"Here you'll need to wear this on your ear" he said handing her an ear piece.

She equipped it on herself then waiting for the next set of directions.

"Now Potts you only have to walked two blocks down, he's at this party in a bistro someone rented, all you have to do is get acquainted with him" he said.

"Affirmative" she said.

"Your also going to need this" he said giving her a gun.

"This is suppose to be strapped around your leg under your coat" he said.

She took it and slipped it up her leg.

"Alright we'll be listening in from across the street in a van, now go" he said.

"Hey be careful" Virgil said.

"Yeah, yeah" she said.

She nodded then started walking down the sidewalk with her hands in the jackets pockets.

She could hear the music booming from a block away. The sidewalks and streets were very crowded. Taxis honking people talking with others or on their cellphones. She finally made it to the bistro and entered. People were partying wildly. She tried blending in with everyone making all of them think she was invited. She looked for the suspect who was supposed to be wearing a blue shirt and Nikes. He was spotted sitting with another girl.

"Time to think Pepper..." She said.

She sat right in front of the mans view and pulled out her phone pretending to text or go on the Internet. The girl eventually left to go to the bathroom and that's when he noticed her. He waited for a few minutes then made his move. He walked up to her.

"This seat taken?" He asked.

"No not at all" she said.

He sat down across from her.

They were sitting at a tall table.

"So what's a beauty like you at a place like this?" He flirted.

"Well one of my friends invited me so I thought why not" she said.

"Where's your friend?" He asked.

"She should be around here somewhere" she said pretending to look for her 'friend.'

"Potts?" Said a familiar voice.

"Oh...crap..." She groaned.

"Hey...Whitney how's it going?" She asked.

"What are you doing here? I didn't know you knew Allie?" Whitney asked.

"I don't another friend invited me" Pepper said.

"Who invited you?" She asked.

"Uhhh..." She said as she was quickly scanning the room for someone she knew.

"Um..uh oh Jessica asked me!" She said.

"Jessica...that's funny I thought you two were like not friends a few days ago?" Whitney said.

"We made up now just go away" Pepper said.

"Fine I will!" Whitney snapped then left.

"Hey lets go to the roof it's more calm up there" said the man.

She nodded then followed him up the stairs. Once they reached the top she walked over to the edge and looked down. They were pretty high up. Suddenly she heard a door slam.

"Alright lady who are you" he asked.

She turned around.

"What do you mean?" She asked.

"I don't play games now spit" he said pulling out a gun.

She smiled.

"I'm sorry" she said.

She walked to a spot her FBI team couldn't see her.

"I came because I want to know who YOU are" she said.

"And why?" He asked aiming the gun at her forehead.

"Because I want to know what you do with your victims..." She said.

His eyes widened.

"How do you know!" He asked.

"Is it true that you are making illegal softwares and trapping girls in your basement?" She asked.

"You know I think ill tell you because your going to die anyway" he said.

"So is that a yes?" She asked.

"You bet" he said.

"You dumb idiot" she said then whipped off her coat.

She started running as he tried to shoot her. She ran behind the wall of the entrance to the roof. She clutched her armored arm then took a deep breath.

"Come out!" He yelled.

She swiftly came out of hiding and shot the gun out of his hands.

He panicked.

"How did you-" he turned around and ran to the edge.

"It's over the FBI knows everything and they closed in on the bistro exits" she said.

"I'm not going to jail!" He yelled.

"I think you will" she said walking up to him.

"If I go down you go down!" He yelled tripping her then jumped off the building.

"Whoa!" She yelled when she fell over.

She was plunging to her death when by a miracle she was caught.

"Tony!" She yelled.

"I told you I would be watching" he said.

Rhodey came along and caught the criminal.

As he flew up she noticed something on the buildings roof.

"Wait go back to the roof..." She said.

He landed on top of the roof and set her down. She walked over to the un identified object and picked it up.

"It's his cell phone..." She said.

"Wait maybe he has some of his software on it so keep it I wanna see what he's up to" Tony said.

"Tony we can't steal evidence!" She said.

"Whatever just this once" he said.

"...I hope you know what you're doing" she said.

"Of course I do" he said.

"Alright well could you drop me off down there? I have to give a report then I get to leave" she said handing him the phone.

"One condition" he said placing the phone in his special compartment.

"Which would be?" She asked.

He opened up his face plate and tapped his lips with his finger.

"What if the cops burst through that door?" She asked playfully.

"I highly doubt it" he said.

Once she got close enough he pulled her into his arms and kissed her.

"Still our little secret" he said smiling.

"Not for long if you keep asking for affection in public" she said.

"Do you think we could continue this at my house then?" he asked smirking as he picked her up.

She laughed. "Whatever" she said.

"Ill take that as a yes" he said.

He closed his face plate before he took off. He landed right in front of the scene.

"Thank you so much iron man" said Virgil.

"No problem sir" Tony said then took off along with Rhodey who had finished talking with an officer.

"Now Patricia once you finish the report you can go home ill actually be home later than you though" Virgil said.

"That's alright ill be at Tonys house" she said.

"I don't know...you alone at a boys house...that doesn't mix with me" he said.

"We're just friends and besides we gotta study for our test next week" she said.

"Pfft I know that's a total lie but fine go ahead I guess your at that age" he said.

"Dad!" She yelled.

"Alright now go before I change my mind!" He laughed.

With that she left back to the hideout to do her report.

...

About an hour of signing forms and writing her full report she finally finished and filed it into the computer.

"Thank you Miss Potts your done for today" said the director.

"No problem" she said then left to Tonys place.

Once she got there she pulled out her phone and texted him.

**10/7/13 11:47 PM**

**I'm outside, is your dad home?**

**IchLiebeDich[3] **

**10/7/13 11:48 PM**

**Nope, come in you know where the key is **

**Stark: Smartest sexiest man you know**

**10/7/13 11:50 PM**

**Uh what's up with that sig? **

**IchLiebeDich[3] **

**10/7/13 11:52 PM**

**I speak the truth and oh like saying I love you in German is any better and I've been meaning to talk to you about that! What if you have a German guy friend and he takes that the wrong way?**

**Stark: Smartest sexiest man you know**

She walked up the stairs to his room and opened the door. Tony was on his bed laying on his side in a pose with rose pedals and vanilla candles lit. She started giggling.

"What is all this?" She asked.

"What I can't do special things?" He asked getting up.

"I'm not saying you can't I just-" he stopped her with his finger placed on her lips.

"Don't be so nervous it's only me" he said from sensing her tension and seeing her flushed face.

She let out a laughing breath then placed her lips on his and kissed him for a moment until she was lifted from her feet. He sat on his bed with her on his lap in a straddling position when they heard a phone flash an alert.

"Ignore. It" Tony said between the kiss.

"I. Can't. What if it's my. Father" she said in between kissing.

He groaned once he was forced to let her go. She looked at her phone.

"Was it your phone? It wasn't mine" she said.

"Wasn't mine either I have it on silent" he said.

She thought for a moment.

"Where's the guy's phone?" She asked.

"Over there on the counter" he said.

She picked it up and saw a text message, she opened it and read it.

"The chip is in the phone case...do not press the mini blue button what ever you do" she read.

She immediately removed the case from the phone and a rectangular chip fell out. She picked it up carefully and examined it.

It had a big blue glowing hole in the center.

"What is this..." She asked.

Tony got up and walked over to her.

"Something tells me it's trouble here give it to me I don't think we should toy with this" he said.

"Whoa wait!" She said as he was about to take the chip away.

"We gotta figure out what this is!" She said.

Her thumb accidentally moved to a certain spot on the chip then it started to do something weird which made her drop it.

"What's it doing?" She asked.

Suddenly a beam shot from it at Pepper. She was being materialized.

"Pepper!" He yelled.

Soon she disappeared into the chip.

"Oh my god what the hell just happened..." He said.

**(So what did ya think? Basically Pepper is now a cortana LOL I love cortana she is my favorite character in halo and well I got this idea when I watched tron legacy and all the blue lights made me think of her.(The movie was OKAY but it's not my favorite) so review tell me what you think was it good? Or was it bad? Whatever it is just spit it into the reviews! Thank you)**


	2. Chapter 2

**(Look I updated! XD ****I didn't know how to describe cortana so don't go "what the hell? XD" when you read what I described virtual Pepper to look like in the story cause I copied and pasted that part from wiki LOL but of course I edited it a bit because in the description it said roughly in her early 20's umm no in this story Pepper is only 17 (I hope I didn't already set an age because I didn't review over this story XD). Alright well enjoy!)**

"Pepper! Pepper can you hear me?!" Tony yelled.

He picked up the glowing chip and examined it.

"Alright lets get you to the armory" he said.

He dropped the chip in his pocket then armored up and flew from his window to the armory.

"Call Rhodey" he said.

"Calling..." Said the computer.

"Hey man what's up?" Rhodey asked.

"Rhodey we have a serious problem alright Pepper is in big trouble I need you to meet me at the armory ASAP!" Tony said.

"Aw man what did she do this time?" Rhodey asked.

"Just meet me there!" Tony said then hung up.

Once he got there he armored down then took out the chip and placed it under a scanner.

"Computer scan the chip" he said.

"Scanning...scan completed" said the computer.

"I wanna know where this thing came from" he said.

"Origins are traced back to a hidden lab in Russia" said the computer.

"Is there a way to release a human trapped inside it?" He asked.

"Determined by the scan results there is no way to release a human from its virtual state but you are able to access the person through a terminal which one is located in the hidden Russian lab" said the computer.

"Alright I'm here!" Rhodey yelled as he ran through the doors.

"Rhodey get in your armor we're heading to Russia" Tony said.

"W-What! Why?" Rhodey asked.

"Ill explain on the way!" Tony said.

"No you said you would explain now so do it!" Rhodey yelled.

Tony sighed in frustration then explained all the events that led up to now.

"Understand now?" He asked.

"So your saying Pepper is trapped in a little chip?" Rhodey asked.

"Yes and there's a lab in Russia that manufactured this crap and they are gonna help us get her out" Tony said.

"Alright then lets go I gotta be back before mom notices" Rhodey said.

They quickly armored up, Tony made sure the chip was secure in his armors secret compartment.

"Don't worry Pep I'll get you out soon" he said.

They blasted into the sky.

"Computer orbital launch now, have the war machine follow my lead" he said.

"Launching in 3,2,1" the computer said.

The armors blasted off in space to Russia.

...

About an hour or two later they finally made it.

"Show me the lab coordinates" Tony said.

The computer pulled up the location and he followed them. They were led to a door in a hidden alley. The door was already opened so they let themselves in.

"Whoa dude..." Rhodey said.

The lab was destroyed, they saw a few dead bodies laying around. Computers were smashed, desks were broken along with chairs, it pretty much looked like the beasts room in beauty and the beast except maybe more trashed.

The boys walked through the lab looking for things that might help them.

"What's this?" Tony said examining a strange object.

"Wait this is...the terminal!" He said excitedly.

"He took out the chip then inserted it.

Right when he inserted it a hologram was projected. It was a nude female human (albeit censored by geometric patterns over her body), with purplish/bluish skin, shoulder length purplish/bluish hair cut shorter at the back, and blue symbols scrolling down her body. She was staring right at Tony.

"P-Pepper?" Tony said.

"This...is amazing!" She yelled.

"Tony I have so much to tell you being inside this chip I-It's amazing! I know everything! All the knowledge it's magical in an instant I know everything about the world n-no! I know everything about everything!" She said.

"Well listen right now we're in Russia in a lab here and we need to figure out how to get you out of that chip" he said.

"I kinda don't wanna get out..." She said.

"What! You have to! You can't just stay in there forever" he said.

"I've never felt so good Tony this is truly the most magical thing I've ever experienced! Every minute I'm getting new information" She said.

Rhodey walked up to them.

"Is that Pepper?" He asked.

"Yup!" Pepper said.

Rhodey looked up and down then looked away in embarrassment.

"Tony do you not realize she doesn't have any clothes?" He said.

Pepper looked down then Tony started to notice. His whole face turned into a tomato then he quickly turned away.

"Well...you can't see my 'features' so I guess it's alright" she said quoting the features.

"Uhhhummm" Tony said.

"Guys whatever you can't see anything it's just an outline" she's said putting her hands on her hips and rolling her eyes.

"Alright I'm gonna pretend your wearing an invisible bikini...you can't see it but it's actually covering you...yeah that works!" He said turning around.

"Alright you clowns what are you gonna do about this?" She asked.

"Well the computer said there's no way to release you from the chip but I know there's a way there's got to be some sort of way" he said.

"Well there's nothing yet about that in my knowledge archive" she said.

"I thought you said you knew everything" he said.

"I might've exaggerated? I told you I get updates every minute!" She said.

"Mhm..." He said.

"Oh please I know far more than you!" She said.

"MHM..." He said.

"I can hack anything, get any code or any information I want, I can hack freaking NASSA without them tracing me with ease!" She said.

"Ill believe it when I see it and plus I used to hack them just for fun!" he said.

"Want me to access the mars rover? I can give you a view of what it's looking at?" She asked.

"No Pep don't get yourself in trouble" he said.

"Just for that I'm doing it! Accessing..." She said.

A few seconds later she projected what the rover was looking at through a functioning computer screen.

"With ease!" She said.

Rhodey ran over to it.

"This is amazing Pepper! Wow so that's what mars looks like right now..." He said.

"Alright Pepper you proved your point now get off their servers" he said.

She crossed her arms and rolled her eyes.

The connection was cut.

"Aw!" Rhodey whined.

"Come on we gotta figure out at least a way to project you again" Tony said.

"Actually you can install me into your suit, I'm compatible with it" she said.

"Really?" He asked.

"Yup just yank me then insert me into the suit" she said.

"Well alright then" he said.

Tony yanked the chip out then inserted it into the back of his neck where discs usually get imported.

"Analyzing...disc accepted" Said the computer.

"Tony can you hear me?" Pepper asked.

"Yeah I could hear you fine it worked" he said.

"We aren't going to find anything that's going to help us here we need to go back home to figure something out" she said.

"Rhodey we're going home lets go" Tony said.

...

It was three in the morning when they got half way back home. Tony was checking up on some stuff in his suit during orbital launch which automatically auto piloted for him.

"Tony...I'm sorry this happened it was my fault for messing with the chip" she said.

"It's alright Pep mistakes happen" he said.

She projected herself through the screen he was looking at.

"This was a big mistake what if I'm stuck like this forever? I like being smart and all but I like being human more actually" she said.

"Pepper your not going to be stuck like that forever I'm gonna do everything I can to bring you back" he said.

"I wish I could hug you..." She said

"I wanted to kiss you when I finally got a hold of you but you were just a hologram...I couldn't touch you and you were so little not human size at all" he said.

"I'm sorry..." She said.

"But that's okay because once I free you ill do everything I wanted to do" he said.

"I'm looking forward to it..." She smiled.

**(Alright finally I'm so happy I updated! I'm hoping to get around "this is the part of me" cause I just need to do one more chapter then that's done! Anyways REVIEW! :D)**


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